The golden age of forensic Y-STR typing –
new markers, new databases, new technologies
Lutz Roewer, Dept. Forensic Genetics
Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
System
DYS19
DYS389I
DYS389II
DYS390
DYS391
DYS392
DYS393
DYS385ab (2)
DYS437
DYS438
DYS439
DYS448
DYS456
DYS458
DYS635
YGATAH4
DYS570
DYS576
DYS533
DYS481
DYS549
DYS643
DYS460
DYS627
DYS518
DYS449
DYF387S1ab (2)
DYF399S1 (3)
DYF403S1 (3)
DYF404S1 (2)
DYS526
DYS547
DYS612
DYS626
DYS464 (4)
Minimal
Haplotype
x
x
x
x
x
x
x
PowerPlex Y (12 Loci)
Promega
x
x
x
x
x
x
x
x
x
x
x
Y-Filer (17 Loci)
Applied Biosystems
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
PPY23 (23 Loci)
Promega
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
YFiler plus beta (27 Loci)
Commercial +
Applied Biosystems
add. Y-STRs (45 loci)
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Really fast mutating Y-STR markers are very rare
Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, Choi Y, van Duijn K, Vermeulen M, Brauer S, Decorte R, Poetsch M, von Wurmb-Schwark N, de
Knijff P, Labuda D, Vézina H, Knoblauch H, Lessig R, Roewer L, Ploski R, Dobosz T, Henke L, Henke J, Furtado MR, Kayser M (2010) Mutability of Y-chromosomal
microsatellites: rates, characteristics, molecular bases, and forensic implications. Am J Hum Genet 87(3):341-53.
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Family analysed with 45 markers –
patrilineage resolved with 2 mutations
5
7
6
3
8
9
I
4
4
8
3
8
9
I
I
1
9
3
9
1
4
8
1
5
4
9
5
3
3
4
3
8
4
3
7
5
7
0
6
3
5
3
9
0
4
3
9
3
9
2
6
4
3
3
9
3
4
5
8
3
8
5
a
b
4
5
6
G
A
T
A
H
4
6
2
7
4
6
0
5
1
8
4
4
9
3
8
7
S
1
5
2
6
a
5
2
6
b
6
2
6
3
9
9
S
1
6
1
2
5
4
7
4
0
4
S
1
4
0
3
F
S
G
DYS391 µ=2.54 x 10-3
DYS626 µ=1.22 x 10-2
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
• Yfiler® Plus
• 25 marker, 2 bilocal
• 6 dye matrix
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Ranking of mutation rates (Yfiler® Plus)
Loci
dys438
dys392
dys393
dys437
dys448
dys390
dys385
dys19
ygatah4
dys391
dys389i
dys635
dys389ii
dys456
dys481
dys533
dys439
dys460
dys458
dys518
dyf387S1ab
dys576
dys570
dys627
dys449
Mutation Rate [95% CI]
2,96E-04
4,04E-04
1,09E-03
1,19E-03
1,65E-03
2,06E-03
2,30E-03
2,32E-03
2,47E-03
2,54E-03
2,68E-03
3,72E-03
3,78E-03
4,19E-03
4,97E-03
5.01E-03
5,35E-03
6,22E-03
6,74E-03
1,84E-02
1,59E-02
1,43E-02
1,24E-02
1,23E-02
1,22E-02
Meioses
10122
14867
13713
10101
6678
15061
25620
15539
7709
14935
13788
7525
13759
6678
1744
1730
10096
1717
6677
1556
1804
1727
1426
1766
1617
Position[MutRate]
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
Group[MutRate]
slow
slow
slow
slow
slow
medium
medium
medium
medium
medium
medium
medium
medium
medium
medium
medium
medium
medium
medium
fast
fast
fast
fast
fast
fast
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Continental proportions of distinct haplotypes
determined with slow, middle and fast mutating marker sets
continents
100%
90%
80%
70%
60%
fast mut.
50%
middle mut.
40%
slow mut.
30%
20%
10%
0%
N=18863
N=445
N=2829
N=11830
N=1183
N=2576
Overall
Africa
Asia
Europe
Latin America
North America
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Increased discrimination
18863
0
n=8066
n=10375
n=10945
n=16130
n=18118
N=18863
MHT
SWGDAM
PPY12
Yfiler
PPY23
sample size
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Local Y-STR diversity differs between continents
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Growth of the YHRD (2000-2014)
140000
120000
All haplotypes
Haplotypes 17 loci
100000
Haplotypes 23 loci
Haplotypes with Y-SNPs
80000
60000
40000
20000
r45
r43
r41
r39
r37
r35
r33
r31
r29
r27
r25
r23
r21
r19
r17
r15
r13
r11
r8,9
r5
r3
release1
0
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Count Estimates
Augmented
Pˆ (T  h0 | S  h0 ) 
23 loci
17 loci
9 loci
1
N 1
Count
frequency
0/19,593
5.1 x 10-5
0/71,246
1.4 x 10-5
260/125,700 2.1 x 10-3
Choose the most informative haplotype format
in the largest available database!
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Frequency estimation methods
Counting methods
• Augmented counting
(1/n+1)
• Counting with database
inflation (Brenners κ)
Methods taking evolutionary distance
between haplotypes into account
• Surveying method (Krawczak)
• Coalescence based
estimation (Caliebe)
• Discrete Laplace method
(Andersen)
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Case-sensitive workflow (touch DNA, mixture expected)
Autosomal analysis
Y chromosomal analysis
Mixed female/male profile
Male profile
Database (YHRD) frequency
Autosomal male
profile clearly
identifiable
Report
National Police
Database
Direct matching possible?
Report
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Charité Pilot study to evaluate the workflow:
40 sexual crimes with only „touch“ DNA (2011)
40 cases
8 cases
Individual male
autosomale profile
10 cases
Informative
YSTR Profile
22 cases
inconclusive
Report with
YHRD match statistics
National Police
Database
Number of
informative profiles
doubled
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2013
Casework statistics since implementation of the PPY23 kit
(08/2012 bis 02/2014)
160 cases
(1038 contact stains)
autosomal
No male admixture
observed in the
Amelogenin system
30%
29% (=14 delicts)
with Y-Profil
Y-chromosomal
Additional Y peak
in Amelogenin
70%
37.5% informative for the
male component
No Y profile
(11%)
Y profile
observed
(89%)
informative Y
profile 58%
Single source
Y profile
(>20 Y-STRs)
39%
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Case example 1: touch stain on fabric in a sexual assault case
Autosomale Analyse
• Nur ♀-Komponente, ohne Hinweis auf ♂Beimischung im Amelogenin
Y-chromosomale Analyse
• Vollständiges Y-chromosomales Einzelprofil
in 23 loci
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Case example 2: touch stain on fabric in a child abuse case
 Yfiler + SNaPshot
 9/16 Y-STRs detectable
 Haplogroup I (M170)
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Case example 2 (continuing): Prediction of ancestry
Haplogroup I (I2a) can also be
reliably predicted from YHRD data
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Case example 3: Serial rape - linking 3 crime scenes
DYS
389I
DYS
448
DYS
389II
DYS
19
DYS
391
DYS
438
DYS
437
DYS
635
DYS
390
DYS
439
DYS
392
DYS
393
DYS
458
DYS
385ab
DYS
456
GATA
H4
Case1
13
19
29
14
10
12
15
24
22
12
13
13
17
11,14
16
12
Case2
13
19
29
nd
10
nd
15
nd
nd
nd
nd
13
17
11,14
16
nd
Case 3
13+
19+
29+
14+
10+
12+
15+
24
22+
12+
13+
13
17
11,14+
16+
12+
Consensus profile
Suspect
DYS
389I
DYS
448
DYS
389II
DYS
391
DYS
437
DYS
393
DYS
458
DYS
385ab
DYS
456
13
19
29
10
15
13
17
11,14
16
12
19
27
11
15
13
16
11,14
14
Exclusion of the suspect
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Is NGS the future for complete resolution
of male relatives ?
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Next generation sequencing
• 13 generations
• 10 Mb (of 24 MB NRY)
sequenced
• 67 STRs identical
• 4 SNPs different
• Potentially long
sequence reads more
variable than STRs
Xue Y, Tyler-Smith C 2009
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Summary
• Wider acceptance of forensic Y chromosome analysis due to a new generation
of diagnostic kits with high discriminative power and much improved
performance
• Complete resolution of distant relatives in most populations
• a proportion of close relatives can be differentiated
• Adaptation of the workflow, otherwise you‘re losing evidence!
• Necessity to employ statistics (LR) to evaluate the match probability
• Haplotype databases accomodate the profiles of the new generation kits
(www.yhrd.org)
• Y-STRs are included in different National DNA Databases (USA, Netherlands,
Austria)
For Forensic or Paternity Use Only.
Yfiler is a trademark of Thermo Fisher Scientific and its subsidiaries.
©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014
Disclaimers
For Forensic or Paternity Use Only.
Yfiler is a trademark of Thermo Fisher Scientific and its subsidiaries.